[gmx-users] AMBER99sb-ILDN force field and TIP4P water model

[Mahboobeh Eslami]

dear timo
Please send me further details. I'm not a professional.
Thanks and regards




On Thursday, November 28, 2013 4:28 PM, Timo Graen <tgraen at gwdg.de> wrote:
 
On Thu 28 Nov 2013 01:22:16 PM CET, Mahboobeh Eslami wrote:

> Hi GMX Users, please help me
> I am trying to begin a simulation of a protein and ligand coplex by gromacs4.6.3.
>
> I am using AMBER99sb-ILDN force field and TIP4P water model. However,
> I am facing a problem in the ion adding step.
>
> when  I issue the grompp command to generate the necessary .tpr file
> for simulation to be utilised by genion tool, I get the following
> error :
>
> Fatal error:
> number of coordinates in coordinate file (solv.gro, 102546)
> does not match topology (topol.top, 133916)
>
> whe i use tip3p, i don't get error.
>
> Thank you very much

Use share/gromacs/top/tip4p.gro when generating the simulation box, 
tip4p has an aditional interaction site

best
timo

--
--
T.M.D. Graen
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics Department, 105 00
Am Fassberg 11
37077 Goettingen, Germany
Tel.:  ++49 551 201 2313
Fax:  ++49 551 201 2302
Email: tgraen at gwdg.de